[English] 日本語
Yorodumi
- PDB-6nzj: Structural Analysis of a Nitrogenase Iron Protein from Methanosar... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nzj
TitleStructural Analysis of a Nitrogenase Iron Protein from Methanosarcina acetivorans: Implications for CO2 Capture by a Surface-Exposed [Fe4S4] Cluster
ComponentsNitrogenase iron protein
KeywordsOXIDOREDUCTASE / Nitrogenase / Iron Protein / FeS cluster / Methanosarcina acetivorans / electron transport
Function / homology
Function and homology information


nitrogenase / : / nitrogenase activity / nitrogen fixation / 4 iron, 4 sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
Nitrogenase iron protein NifH / NifH/frxC family / NifH/chlL conserved site / 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family / NifH/frxC family signature 2. / NifH/frxC family signature 1. / NIFH_FRXC family profile. / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold ...Nitrogenase iron protein NifH / NifH/frxC family / NifH/chlL conserved site / 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family / NifH/frxC family signature 2. / NifH/frxC family signature 1. / NIFH_FRXC family profile. / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Nitrogenase iron protein
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRettberg, L.A. / Kang, W. / Stiebritz, M.T. / Hiller, C.J. / Lee, C.C. / Liedtke, J. / Ribbe, M.W. / Hu, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1651398 United States
CitationJournal: Mbio / Year: 2019
Title: Structural Analysis of a Nitrogenase Iron Protein from Methanosarcina acetivorans: Implications for CO 2 Capture by a Surface-Exposed [Fe 4 S 4 ] Cluster.
Authors: Rettberg, L.A. / Kang, W. / Stiebritz, M.T. / Hiller, C.J. / Lee, C.C. / Liedtke, J. / Ribbe, M.W. / Hu, Y.
History
DepositionFeb 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 29, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.4Sep 30, 2020Group: Database references / Derived calculations / Category: citation / struct_conn
Item: _citation.title / _struct_conn.ptnr1_auth_asym_id ..._citation.title / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.5Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nitrogenase iron protein
B: Nitrogenase iron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1876
Polymers58,5472
Non-polymers6404
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-93 kcal/mol
Surface area19370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.169, 96.169, 320.244
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-425-

HOH

-
Components

#1: Protein Nitrogenase iron protein / Nitrogenase Fe protein / Nitrogenase component II / Nitrogenase reductase


Mass: 29273.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A) (archaea)
Strain: ATCC 35395 / DSM 2834 / JCM 12185 / C2A / Gene: nifH, MA_3895 / Variant: ATCC 35395 / DSM 2834 / JCM 12185 / C2A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8TJ93, nitrogenase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Nitrogenase Fe protein / Nitrogenase component II / Nitrogenase reductase


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66.31 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 8 / Details: PEG 3350, carbonate, dithionite

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 21, 2017
RadiationMonochromator: Double-crystal Si(111) and multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→83.29 Å / Num. obs: 40175 / % possible obs: 100 % / Redundancy: 11.9 % / Biso Wilson estimate: 45.3 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.111 / Net I/σ(I): 5.4
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 11.2 % / Num. unique obs: 35369 / CC1/2: 0.81 / Rrim(I) all: 0.781 / Χ2: 1 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
MOSFLM7.0.062data reduction
SCALA7.0.062data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CP2

1cp2


Resolution: 2.4→83.285 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.41
RfactorNum. reflection% reflectionSelection details
Rfree0.2164 1805 5.1 %Random selection
Rwork0.1864 ---
obs0.188 35369 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→83.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3952 0 23 170 4145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054026
X-RAY DIFFRACTIONf_angle_d0.7045462
X-RAY DIFFRACTIONf_dihedral_angle_d4.662395
X-RAY DIFFRACTIONf_chiral_restr0.047648
X-RAY DIFFRACTIONf_plane_restr0.004710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.46490.3181360.25482510X-RAY DIFFRACTION100
2.4649-2.53740.27071450.24142510X-RAY DIFFRACTION100
2.5374-2.61930.27011120.2312526X-RAY DIFFRACTION100
2.6193-2.7130.28191320.22682529X-RAY DIFFRACTION100
2.713-2.82160.2561370.22382558X-RAY DIFFRACTION100
2.8216-2.950.25661310.21682509X-RAY DIFFRACTION100
2.95-3.10550.21491250.21542593X-RAY DIFFRACTION100
3.1055-3.30010.26981570.21542533X-RAY DIFFRACTION100
3.3001-3.55490.22061390.19222580X-RAY DIFFRACTION100
3.5549-3.91270.20721380.16282568X-RAY DIFFRACTION100
3.9127-4.47880.151440.14922622X-RAY DIFFRACTION100
4.4788-5.64270.1741510.1532669X-RAY DIFFRACTION100
5.6427-83.33490.22451580.18372857X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more